Influences of the disease resistance conferred by the individual transgenes, Pi-d2, Pi-d3 and Xa21, on the transgenic rice plants in yield and grain quality

To research possible influences of the disease resistance conferred by different trans-resistance genes on the transgenic rice plants in their yields and grain quality, three transgenic rice lines, including two with the resistance genes Pi-d2 and Pi-d3, respectively, for rice blast, and one with the resistance gene Xa21 for rice bacterial blight, which all showed the highest resistance to their respective pathogen races, were used to analyze and measure their respective characters in yield and grain quality as compared to those of the transgenic control line with the empty vector that was used to transfer Pi-d2, Pi-d3 and Xa21, respectively. Both yield and grain quality of all three transgenic materials with the respective trans-resistance genes decreased significantly. Grain weight per plant of Pi-d2, Pi-d3 and Xa21 transgenic individuals decreased by 7.7%, 29.6 and 44.4%, respectively, compared to the control. Grain quality of Pi-d2 and Pi-d3 transgenic plants were both the third class according to the Industrial Standard, ‘Grain Quality of Edible Rice Variety’ and one class worse than that of the control, but the third class still belongs to edible grains. However, grain quality of Xa21 transgenic plants was too bad to be edible

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

BackgroundOncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance.ResultsIn reference Sample A, we identify more than 40,000 variants down to 1% allele frequency with more than 25,000 variants having less than 20% allele frequency with 1653 variants in COSMIC-related genes. This is 5-100x more than existing commercially available samples. We also identify an unprecedented number of negative positions in coding regions, allowing statistical rigor in assessing limit-of-detection, sensitivity, and precision. Over 300 loci are randomly selected and independently verified via droplet digital PCR with 100% concordance. Agilent normal reference Sample B can be admixed with Sample A to create new samples with a similar number of known variants at much lower allele frequency than what exists in Sample A natively, including known variants having allele frequency of 0.02%, a range suitable for assessing liquid biopsy panels.ConclusionThese new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.Peer reviewe